incl/TopDom.R

In HenrikBengtsson/TopDom: An Efficient and Deterministic Method for Identifying Topological Domains in Genomes

path <- system.file("exdata", package = "TopDom", mustWork = TRUE)

## Original count data (on a subset of the bins to speed up example)
chr <- "chr19"
pathname <- file.path(path, sprintf("nij.%s.gz", chr))
data <- readHiC(pathname, chr = chr, binSize = 40e3, bins = 1:500)
print(data)  ## a TopDomData object

## Find topological domains using the TopDom method
fit <- TopDom(data, window.size = 5L)
print(fit)  ## a TopDom object

## Display the largest domain
td <- subset(subset(fit$domain, tag == "domain"), size == max(size))
print(td) ## a data.frame

## Subset TopDomData object
data_s <- subsetByRegion(data, region = td, margin = 0.9999)
print(data_s)  ## a TopDomData object

vp <- grid::viewport(angle = -45, width = 0.7, y = 0.3)
gg <- ggCountHeatmap(data_s)
gg <- gg + ggDomain(td, color = "#cccc00") + ggDomainLabel(td)
print(gg, newpage = TRUE, vp = vp)

gg <- ggCountHeatmap(data_s, colors = list(mid = "white", high = "black"))
gg_td <- ggDomain(td, delta = 0.08)
dx <- attr(gg_td, "gg_params")$dx
gg <- gg + gg_td + ggDomainLabel(td, vjust = 2.5)
print(gg, newpage = TRUE, vp = vp)

## Subset TopDom object
fit_s <- subsetByRegion(fit, region = td, margin = 0.9999)
print(fit_s)  ## a TopDom object
for (kk in seq_len(nrow(fit_s$domain))) {
  gg <- gg + ggDomain(fit_s$domain[kk, ], dx = dx * (4 + kk %% 2), color = "red", size = 1)
}

print(gg, newpage = TRUE, vp = vp)


gg <- ggCountHeatmap(data_s)
gg_td <- ggDomain(td, delta = 0.08)
dx <- attr(gg_td, "gg_params")$dx
gg <- gg + gg_td + ggDomainLabel(td, vjust = 2.5)
fit_s <- subsetByRegion(fit, region = td, margin = 0.9999)
for (kk in seq_len(nrow(fit_s$domain))) {
  gg <- gg + ggDomain(fit_s$domain[kk, ], dx = dx * (4 + kk %% 2), color = "blue", size = 1)
}

print(gg, newpage = TRUE, vp = vp)